MATPredict · mating-type report

Sschenckii1099-18

MAT locus above the FungiDB annotation (gene by gene)

organism not recorded

Run by MATPredict 0.8.1 (v0.8.1, 3a62e6302b) · database 86f18d232e4f · local NCBI taxonomy snapshot 2026-10-01 · rendered 2026-11-07 01:48 UTC by MATPredict 0.8.1

Result

Mating type

MAT1-1high confidence

Called loci 1

MAT1-1 MAT family · Ascomycota

high confidence
Gene order of the MAT1-1 locus on AXCR01000001MAT1-1 locus: genes from left to right on AXCR01000001, 1,660,765 to 1,705,874: SLA2 (conserved flank, plus strand); MAT1-1-1 (core MAT gene, minus strand); MAT1-1-2 (core MAT gene, minus strand); MAT1-1-3 (core MAT gene, plus strand); MAT1-2-1 (core MAT gene, plus strand); COX13 (conserved flank, minus strand); APN2 (conserved flank, minus strand).1,660 kb1,670 kb1,680 kb1,690 kb1,700 kb1,464.1 kb more to contig end →called locusSLA2: conserved flank, 1,660,765–1,664,229 (+), identity 93.9%, search hit onlySLA2MAT1-1-1: core MAT gene, 1,666,165–1,669,269 (-), identity 44.8%, search hit onlyMAT1-1-1MAT1-1-2: core MAT gene, 1,669,869–1,671,193 (-), identity 34.8%, search hit onlyMAT1-1-2MAT1-1-3: core MAT gene, 1,671,585–1,671,924 (+), identity 61.0%, search hit onlyMAT1-1-3MAT1-2-1: core MAT gene, 1,672,001–1,672,278 (+), identity 41.1%, gene modelMAT1-2-1COX13: conserved flank, 1,697,144–1,698,020 (-), identity 72.6%, search hit onlyCOX13APN2: conserved flank, 1,702,952–1,705,874 (-), identity 61.5%, search hit onlyAPN2
Gene order on AXCR01000001. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on AXCR01000001, 1,658,513 to 1,708,128SPSK_05815 1,654,960-1,659,924 (-): DNA polymerase zeta subunitSPSK_05815SPSK_05860 1,660,765-1,664,229 (+): hypothetical proteinSPSK_05860SPSK_05897 1,666,165-1,669,269 (-): hypothetical proteinSPSK_05897SPSK_06310 1,669,869-1,671,193 (-): hypothetical proteinSPSK_06310SPSK_06759 1,671,585-1,671,924 (+): hypothetical proteinSPSK_06759SPSK_06711 1,674,915-1,675,365 (+): hypothetical proteinSPSK_06711SPSK_05817 1,677,660-1,682,384 (-): hypothetical proteinSPSK_05817SPSK_05913 1,693,223-1,696,175 (+): hypothetical proteinSPSK_05913SPSK_06524 1,697,144-1,698,020 (-): cytochrome c oxidase subunit 6aSPSK_06524SPSK_06719 1,699,292-1,699,729 (-): hypothetical proteinSPSK_06719SPSK_06094 1,700,331-1,702,241 (+): hypothetical proteinSPSK_06094SPSK_05918 1,702,952-1,705,874 (-): AP endonuclease 2SPSK_05918SPSK_05878 1,707,657-1,710,907 (-): C6 transcription factorSPSK_05878
FungiDB release 68 annotation of the same window: gene models from the GFF (filled = CDS, pale = UTR exon, line = intron, arrow = strand). Green genes overlap a MATPredict gene on the same strand; grey genes do not. Click a gene to open it on fungidb.org.
  • core MAT gene
  • conserved flank
  • gene model
  • search hit only
  • MAT1-2-1 is a weak hit to the other idiomorph's gene and was not counted against the call.
Location
AXCR01000001:1,660,765–1,705,874 · 45.1 kb
Own genes
AXCR01000001:1,660,765–1,705,874 · 45.1 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
7 of 7 gene hits
Nearest contig end
1.5 Mb
Region (samtools)
AXCR01000001:1660765-1705874
Idiomorph scores
  • MAT1-1 271.0
  • MAT1-2 37.7

Margin over the next idiomorph: 233.3

Score: bitscore of the best core-gene hit for each idiomorph.

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
SLA2conserved flankhit onlyDIAMOND, proteome93.9cov 100.0%< 1e-1801,162 bits1,660,765–1,664,229 +–230073_uamh-1363_MAT_MAT1-1SPSK_05860
MAT1-1-1core MAThit onlyDIAMOND, proteome44.8cov 50.4%9.8e-81271 bits1,666,165–1,669,269 -–230073_uamh-1363_MAT_MAT1-1SPSK_05897
MAT1-1-2core MAThit onlyDIAMOND, proteome34.8cov 99.1%1.3e-68212 bits1,669,869–1,671,193 -–230073_uamh-1363_MAT_MAT1-1SPSK_06310
MAT1-1-3core MAThit onlyDIAMOND, proteome61.0cov 42.8%7.6e-32103 bits1,671,585–1,671,924 +–230073_uamh-1363_MAT_MAT1-1SPSK_06759
MAT1-2-1core MATother idiomorph, not countedgene modelexonerate41.1cov 58.7%5.6e-0838 bits1,672,001–1,672,278 +261372_suf959_MAT_MAT1-2none
COX13conserved flankhit onlyDIAMOND, proteome72.6cov 67.9%8.6e-49145 bits1,697,144–1,698,020 -–199306_rmscc1040_MAT_MAT1-1SPSK_06524
APN2conserved flankhit onlyDIAMOND, proteome61.5cov 32.5%1.3e-114354 bits1,702,952–1,705,874 -–2903220_liq80xsp_MAT_combinedSPSK_05918

Withheld candidate loci 2

Places with some MAT-gene evidence that did not pass a quality gate. Most genomes have several. They are listed so a known locus can be checked against them, not because they are likely calls.

Reasons: too few of the family's genes found (2).

Show the 2 withheld loci

Withheld loci (2)

familylocationidiomorph genesmodelledreason
MATAXCR01000007:4,188,689–4,191,907MAT1-1MAT1-1-31too few of the family's genes found
MATAXCR01000012:2,997,044–3,002,832MAT1-1MAT1-1-1, MAT1-2-11too few of the family's genes found

Provenance

Genome file
Sschenckii1099-18.genome.fasta
Assembly
16 contigs · 32.4 Mb · N50 4.3 Mb
Genome SHA-256
2a676281fbb42b3cf27507084aeaf0e0d9c4cd4028f0f05e1f4b1510b0b87483
MATPredict
0.8.1 (v0.8.1, 3a62e6302b)
Database
86f18d232e4fe95d · 185 records
Taxonomy
local NCBI taxonomy snapshot 2026-10-01
Parameters
phylum=Ascomycota, phylum_guess={'requested': 'auto', 'status': 'ok', 'usable': True, 'reason': None, 'phylum': 'Ascomycota', 'phylum_taxid': 4890, 'deepest_rank': 'genus', 'routing_taxid': 5152, 'routing_taxid_rank': 'family', 'flags': [], 'gmg_version': 'gmg 0.3.2 (66055154a)', 'index': 'bfd-reps-2026.10.5-s20000.gmgi', 'index_sha256': '0f319567f1cab17643e1daf7ffdc0e3b312bd43913e351568108d67a4a19702c', 'index_spec': 'bfd-reps-2026.10.5-s20000.gmgi', 'note': 'GmG called phylum Ascomycota', 'action': 'routed', 'weak_call_accepted': False, 'genetic_code': 1, 'genetic_code_from': 'family taxid 5152', 'routed_by': 'family taxid 5152 (lineage)'}, genetic_code=1, min_hits=2, require_core_role=True, max_polished_clusters_per_family=6, polish_strong_identity=50.0, polish_core_pair=True, partial_core_policy=off, homothallic_policy=off, confidence_cap_policy=off, cross_family_policy=off, fallback_after_withheld_policy=off, strong_single_gene_policy=off, scoped_roster_policy=off, scoped_roster=off: BGL1,GAP1 not searched, supported_min_bitscore=33.0
Run started
2026-11-07T01:47:41Z
Run time
78 s
Files
detection_report.yaml, detected_loci.gff3

Cite MATPredict as given in CITATION.cff at github.com/stajichlab/MATPredict. The reference records named in the gene tables are curated database entries; each record's metadata cites its source publication.

How to read this report

Idiomorph
The form of the mating-type locus a strain carries (for example MAT1-1 or MAT1-2, Plus or Minus). Basidiomycota HD and PR alleles are named after the reference they match.
High confidence
Every expected core MAT gene was found and modelled, with a conserved flanking gene where the family has one, on one contig.
Medium confidence
The core genes were found, but a gene could not be modelled, no conserved flank was found, or the locus is split (one step down).
Low confidence
A single isolated gene hit, or no core MAT gene.
Model status
Gene model: the reference protein was aligned to the genome to build the gene (exonerate, miniprot). Models differ: the two tools disagree on the structure; the alternate model is shown. Hit only: a search hit with no model, weaker evidence.
Identity
Percent amino-acid identity between the gene (or hit) and the closest reference protein.
Reference record
The curated database record whose protein matched best. Each record's metadata cites the publication or deposit it comes from.

Limits